# RGD-PIPELINE: ftp-file-extracts # MODULE: variants-ver-1.0.1 # GENERATED-ON: 2021/04/10 # PURPOSE: non-synonomous variants for rat strains, extracted from RGD database # CONTACT: rgd.data@mcw.edu # FORMAT: tab delimited text # # SAMPLE: WKY/NHsd (ICL) # SAMPLE-INFO: WKY/NHsd sequenced by UOX # SEQUENCED-BY: University of Oxford (Dr. Dominique Gauguier) # SEQUENCER: Illumina HiSeq 2000 # SECONDARY-ANALYSIS: BWA-0.5.8c, GATK-v1.0.6001, samtools, Picard # GRANT-NUMBER: Wellcome Trust Senior Fellowship (057733) and Wellcome Trust Core Award Grant (075491/Z/04) # WHERE-BRED: Harlan Laboratories # STRAIN-RGD-ID: 61105 # # COLUMN INFORMATION: # #1 VID unique variant id #2 VAR_TYPE variant type:'snv','ins','del' #3 CHROMOSOME chromosome #4 POSITION position on chromosome #5 REF_NUC reference nucleotide #6 VAR_NUC variant nucleotide #7 REF_AA reference amino acid #8 VAR_AA variant amino acid #9 PREDICTION polyphen prediction #10 TRANSCRIPT transcript id #11 POS_NUC nucleotide position of variant relative to 1st nucleotide of CDS #12 POS_AA aminoacid position of variant relative to protein 1st aminoacid